Next generation sequencing (NGS) has revolutionised rare disease diagnostics. Concomitant with advancing technologies has been a rise in the number of new gene disorders discovered and diagnoses made for patients and their families. However, despite the trend towards whole exome and whole genome sequencing, diagnostic rates remain suboptimal. On average, only ~30% of patients receive a molecular diagnosis. National sequencing projects launched in the last 5 years are integrating clinical diagnostic testing with research avenues to widen the spectrum of known genetic disorders. Consequently, efforts to diagnose genetic disorders in a clinical setting are now often shared with efforts to prioritise candidate variants for the detection of new disease genes. Herein we discuss some of the biggest obstacles precluding molecular diagnosis and discovery of new gene disorders. We consider bioinformatic and analytical challenges faced when interpreting next generation sequencing data and showcase some of the newest tools available to mitigate these issues. We consider how incomplete penetrance, non-coding variation and structural variants are likely to impact diagnostic rates, and we further discuss methods for uplifting novel gene discovery by adopting a gene-to-patient-based approach.

中文翻译：

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使用现代测序技术诊断和发现罕见遗传疾病面临的挑战。

下一代测序（NGS）彻底改变了罕见病诊断方法。与先进技术相伴的是，为患者及其家人发现和诊断的新基因疾病的数量有所增加。然而，尽管趋向于全外显子组和全基因组测序，诊断率仍然不是最佳的。平均而言，只有约30％的患者接受分子诊断。最近5年启动的国家测序项目正在将临床诊断测试与研究途径相结合，以扩大已知遗传疾病的范围。因此，在临床环境中诊断遗传性疾病的努力现在通常与为检测新疾病基因而优先考虑候选变体的努力共享。在这里，我们讨论了一些最大的障碍，包括分子诊断和新基因疾病的发现。我们考虑了在解释下一代测序数据时面临的生物信息学和分析挑战，并展示了一些可用于缓解这些问题的最新工具。我们考虑不完整的外显力，非编码变异和结构变异会如何影响诊断率，并且我们进一步讨论了采用基于基因对患者的方法来提升新基因发现的方法。